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- PDB-9h1o: Cryo-EM structure of taxol-microtubules in complex with the C1 do... -

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Basic information

Entry
Database: PDB / ID: 9h1o
TitleCryo-EM structure of taxol-microtubules in complex with the C1 domain of GEFH1
Components
  • Rho guanine nucleotide exchange factor 2
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsSIGNALING PROTEIN / RhoGEF / C1 / Cytoskeleton / Complex
Function / homology
Function and homology information


asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / negative regulation of necroptotic process / cellular hyperosmotic response / positive regulation of axon guidance / regulation of small GTPase mediated signal transduction ...asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / negative regulation of necroptotic process / cellular hyperosmotic response / positive regulation of axon guidance / regulation of small GTPase mediated signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / RHOB GTPase cycle / NRAGE signals death through JNK / RHOA GTPase cycle / bicellular tight junction / microtubule-based process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic microtubule / positive regulation of neuron differentiation / cellular response to interleukin-4 / guanyl-nucleotide exchange factor activity / actin filament organization / intracellular protein transport / : / structural constituent of cytoskeleton / positive regulation of interleukin-6 production / small GTPase binding / microtubule cytoskeleton organization / spindle / ruffle membrane / neuron migration / cell morphogenesis / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / mitotic cell cycle / G alpha (12/13) signalling events / regulation of cell population proliferation / double-stranded RNA binding / microtubule cytoskeleton / cytoplasmic vesicle / microtubule binding / vesicle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / cilium / protein heterodimerization activity / innate immune response / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. ...ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin alpha-1B chain / Tubulin beta-2B chain / Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChoi, S.R. / Blum, T. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Cell / Year: 2025
Title: Structural basis of microtubule-mediated signal transduction.
Authors: Sung Ryul Choi / Thorsten B Blum / Matteo Giono / Bibhas Roy / Ioannis Vakonakis / Dominic Schmid / Nicole Oelgarth / Apisha Ranganathan / Alvar D Gossert / G V Shivashankar / Alfred ...Authors: Sung Ryul Choi / Thorsten B Blum / Matteo Giono / Bibhas Roy / Ioannis Vakonakis / Dominic Schmid / Nicole Oelgarth / Apisha Ranganathan / Alvar D Gossert / G V Shivashankar / Alfred Zippelius / Michel O Steinmetz /
Abstract: Microtubules have long been recognized as upstream mediators of intracellular signaling, but the mechanisms underlying this fundamental function remain elusive. Here, we identify the structural basis ...Microtubules have long been recognized as upstream mediators of intracellular signaling, but the mechanisms underlying this fundamental function remain elusive. Here, we identify the structural basis by which microtubules regulate the guanine nucleotide exchange factor H1 (GEFH1), a key activator of the Ras homolog family member A (RhoA) pathway. We show that specific features of the microtubule lattice bind the C1 domain of GEFH1, leading to the sequestration and inactivation of this signaling protein. Targeted mutations in C1 residues disrupt this interaction, triggering GEFH1 release and activation of RhoA-dependent immune responses. Building on this sequestration-and-release mechanism, we identify microtubule-binding C1 domains in additional signaling proteins, including other guanine nucleotide exchange factors (GEFs), kinases, a GTPase-activating protein (GAP), and a tumor suppressor, and show that microtubule-mediated regulation via C1 domains is conserved in the Ras association domain-containing protein 1A (RASSF1A). Our findings establish a structural framework for understanding how microtubules can function as spatiotemporal signal sensors, integrating and processing diverse signaling pathways to control important cellular processes.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Rho guanine nucleotide exchange factor 2
B: Tubulin alpha-1B chain
A: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Tubulin beta-2B chain
F: Tubulin beta-2B chain
G: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,00921
Polymers308,5957
Non-polymers6,41414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28230 Å2
ΔGint-169 kcal/mol
Surface area90560 Å2
MethodPISA

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Components

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Protein , 3 types, 7 molecules CBADEFG

#1: Protein Rho guanine nucleotide exchange factor 2 / Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell ...Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell nucleolar antigen p40


Mass: 8250.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C1 domain of GEFH1 / Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF2, KIAA0651, LFP40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92974
#2: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#3: Protein
Tubulin beta-2B chain


Mass: 49983.824 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856

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Non-polymers , 5 types, 14 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#8: Chemical
ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H51NO14 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1The C1 domain of GEFH1 in complex with microtubuleCOMPLEX#1-#30RECOMBINANT
2C1 domain of GEFH1ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3Tubulin alpha 1BORGANELLE OR CELLULAR COMPONENT#21NATURAL
4Tubulin beta 2BORGANELLE OR CELLULAR COMPONENT#31NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
21NO
31NO
41NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
43Bos taurus (domestic cattle)9913
54Bos taurus (domestic cattle)9913
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33Escherichia coli BL21(DE3) (bacteria)469008
44Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 6.9
Details: BRB80 buffer 80mM PIPES, 1mM MgCl2, 1mM EGTA, pH 6.9
Buffer component
IDConc.NameFormulaBuffer-ID
180 mMPIPESC8H18N2O6S21
21 mMMagnesium ChlorideMgCl21
31 mMEGTAC14H24N2O101
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: C1 domain of GEFH1 was in complex with microtubules
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4RELION3.0.8CTF correctionGCTF
7Coot0.9.8.95model fitting
9RELION3.0.8initial Euler assignment
10RELION3.0.8final Euler assignment
12RELION3D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 326559 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00521553
ELECTRON MICROSCOPYf_angle_d0.93829296
ELECTRON MICROSCOPYf_dihedral_angle_d6.7452889
ELECTRON MICROSCOPYf_chiral_restr0.0483189
ELECTRON MICROSCOPYf_plane_restr0.0073799

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